@zombeerose
I found using the create jsb pointed to a URL was the simplest.
I've had the sencha create jsb working with my stuff with beta 1 and 2 as well as 1.2.3 version of Sencha command sdk tools.
I'll find the post where I talk in more detail about it.

Ugh, I keep getting this problem as well, I've tried some of these fixes but I have not tried the .senchsdk yet. The issue I am having though is the path issue but it said the build and sign is successful. I'm launching the packaging function from the Architect tool though. I don't know how much of a difference that makes. I'm using the latest version of Architect, SDK and SDK Tools. I get the app create but it throws that error. It however runs in the simulator and I can add it to iTunes but when I try to put it on my device either with iTunes or Xcode, I get install errors. I've literally been racking my brain on this all day. I've got my device set up in the provisioning portal, I've got my cert, I've got my App ID, etc..

cd /Users/ashapiro75/Documents/SenchaProjects/red/
sencha package packager.json
[ERROR] The current working directory (/Users/ashapiro75/Documents/SenchaProjects/red) is not a recognized Sencha SDK or application folder
The application was successfully packaged
The application was successfuly signed
logout

I actually moved the SDK into the /red directory to try that. My app wound up being 187 mb and all it is, is a red screen. That's all I tried to test this with.

So I take the .app that it creates, I put it into iTunes, try to add it to my device and I get an error... I'm about to give up on Sencha, it seems every time I get something down, something else changes and I feel like I am chasing my tail.